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Opened 4 months ago
Last modified 4 months ago
#18425 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.1.1-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
I have the same error many times and some times the system did not respond to selection commands as well, change the syze/color and other atoms instead of the selected ones.
Log:
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/angela/Desktop/Ab_test.cxs format session
Log from Wed Aug 13 13:40:35 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/angela/Desktop/Ab_test.cxs format session
Log from Wed Aug 13 11:43:29 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/angela/Desktop/Structure/Ab_Asps.cxs format session
Log from Wed Aug 13 11:08:38 2025UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/angela/Desktop/Structure/Ab_Asps.cxs format session
Log from Tue Jul 29 16:24:33 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/angela/Desktop/Structure/2024 Gyrase_last-coot7_NH.pdb" format
> pdb
Chain information for 2024 Gyrase_last-coot7_NH.pdb #1
---
Chain | Description
A | No description available
B | No description available
C D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
> set bgColor white
> set bgColor #ffffff00
> hide atoms
> show cartoons
> select /A/B
8201 atoms, 8332 bonds, 2 pseudobonds, 1038 residues, 2 models selected
> color sel bisque
> dssp
> select /C/D
2838 atoms, 2880 bonds, 2 pseudobonds, 358 residues, 2 models selected
> color sel dark slate blue
> select /E/F/G/H
821 atoms, 917 bonds, 40 residues, 1 model selected
> color sel goldenrod
> show sel atoms
> hide sel atoms
> show sel cartoons
> nucleotides sel tube/slab shape box
> show sel cartoons
> show sel atoms
> select /A:DK4
58 atoms, 63 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel orange red
> color sel byhetero
> select /A/B:513
4126 atoms, 4193 bonds, 1 pseudobond, 519 residues, 2 models selected
> select /A/B:Asp
4375 atoms, 4411 bonds, 1 pseudobond, 550 residues, 2 models selected
> select /A/B:Asp513
4118 atoms, 4186 bonds, 1 pseudobond, 518 residues, 2 models selected
> select /C/D:513
1427 atoms, 1447 bonds, 1 pseudobond, 180 residues, 2 models selected
> show sel atoms
> undo
> select /C:513
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:513
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> style sel stick
Changed 8 atom styles
> style sel ball
Changed 8 atom styles
> color sel teal
> select /D:513
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 8 atom styles
> color sel teal
> select clear
> select /A:DK4
58 atoms, 63 bonds, 1 residue, 1 model selected
> style sel ball
Changed 58 atom styles
> select clear
> open 7z9c
7z9c title:
E.coli gyrase holocomplex with 217 bp DNA and albicidin [more info...]
Chain information for 7z9c #2
---
Chain | Description | UniProt
A C | DNA gyrase subunit A | GYRA_ECOLI 2-875
B D | DNA gyrase subunit B | GYRB_ECOLI 2-804
E | DNA (5'-D(P*AP*AP*AP*TP*CP*TP*GP*TP*GP*CP*GP*GP*GP*T)-3') |
F | DNA (5'-D(P*AP*GP*AP*AP*TP*CP*AP*GP*GP*CP*AP*TP*AP*A)-3') |
G | DNA (5'-D(*AP*AP*TP*CP*AP*CP*CP*CP*GP*CP*AP*CP*AP*GP*AP*TP*TP*T)-3') |
H | DNA (5'-D(*GP*AP*TP*TP*TP*TP*AP*TP*GP*CP*CP*TP*GP*AP*TP*TP*CP*T)-3') |
Non-standard residues in 7z9c #2
---
BWH — albicidin
MG — magnesium ion
> hide #!1 models
> show #!1 models
> mmaker # to #1 show alignment true
> matchmaker # to #1 show alignment true
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> mmaker # to #1 showAlignment true
> matchmaker # to #1 showAlignment true
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> mmaker # to #1 show Alignment true
> matchmaker # to #1 show Alignment true
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> mmaker # to #1
> matchmaker # to #1
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> mmaker #2 to #1 show Alignment true
> matchmaker #2 to #1 showAlignment Alignment true
Invalid "showAlignment" argument: Expected true or false (or 1 or 0)
> mmaker #2 to #1 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2024 Gyrase_last-coot7_NH.pdb, chain A (#1) with 7z9c, chain A
(#2), sequence alignment score = 1956.3
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 2024 Gyrase_last-coot7_NH.pdb
#1/A, 7z9c #2/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 441 pruned atom pairs is 0.933 angstroms; (across all 511 pairs:
1.677)
> hide #!1 models
> hide #!2 atoms
> show #!2 cartoons
> color lavender
> color pale goldenrod
> color palegreen misty rose
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color misty rose
> color light salmon
[Repeated 1 time(s)]
> color light pink
> show #!1 models
> color #1/A/B bisque
> color #1/C/D dark slate blue
> color #1/D dark slate blue
> color #1/c dark slate blue
[Repeated 1 time(s)]
> color #1/C dark slate blue
> color #1/D dark slate blue
> color #1/B bisque
> select #1/A:DK4
58 atoms, 63 bonds, 1 residue, 1 model selected
> color sel orange red
> style sel ball
Changed 58 atom styles
> color sel byhetero
> select #2/JWH
Nothing selected
> select #2/JWH
Nothing selected
> show atoms
> undo
> select #2:JWH
Nothing selected
> show atoms
> undo
> select #1/E/F/G/H
821 atoms, 917 bonds, 40 residues, 1 model selected
> nucleotides sel tube/slab shape box
> show sel atoms
> color sel goldenrod rod
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel goldenrod
> select clear
> select #2/E/F/G/H
2029 atoms, 2183 bonds, 56 pseudobonds, 66 residues, 2 models selected
> nucleotides sel tube/slab shape box
> show sel atoms
> select #2/JWH
Nothing selected
> show atoms
> undo
> select #2/BWH
Nothing selected
> show atoms
> undo
> dssp
[Repeated 2 time(s)]
> select #1/C:513
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel teal
> color sel byhetero
> select #1/D:513
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel teal
> color sel byhetero
> select clear
> select #2:BWH
62 atoms, 66 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel grey
> color sel byhetero
> style sel ball
Changed 62 atom styles
> select clear
> select #2/B:500
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 12 atom styles
> color sel byhetero
> select #2/D:500
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 12 atom styles
> color sel byhetero
> select clear
> select #2/MG
Nothing selected
> select #2:mg
2 atoms, 2 residues, 1 model selected
> style sel sphere
Changed 2 atom styles
> color sel green
> color sel byhetero
> hide #!1 models
> select #2D:500
Expected an objects specifier or a keyword
> select #2/D:500
12 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/B:500
12 atoms, 11 bonds, 1 residue, 1 model selected
> delete sel H
Expected a keyword
> delete H
> select #2/C:500
9 atoms, 8 bonds, 1 residue, 1 model selected
> delete H
> show #!1 models
> view sel
[Repeated 1 time(s)]
> select clear
> view
> select #1/505-518
Nothing selected
> select #1/D:505-518
104 atoms, 104 bonds, 14 residues, 1 model selected
> select #1/D:507-516
71 atoms, 70 bonds, 10 residues, 1 model selected
> select #2/A-D
14660 atoms, 14892 bonds, 10 pseudobonds, 1849 residues, 2 models selected
> color sel khaki
> color sel tan
> select clear
> select #2:BWH
62 atoms, 66 bonds, 1 residue, 1 model selected
> color sel grey
> style sel ball
Changed 62 atom styles
> color sel byhetero
> select clear
> select #2/B:500
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #2/D:500
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #2/HOH
Nothing selected
> select #2/MG
Nothing selected
> select #2:MG
2 atoms, 2 residues, 1 model selected
> show sel sphere
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show sel Sphere
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show sel atoms
> color sel green
> color sel lime
> color sel lawn green
> color sel lime
> select #2:HOH
10 atoms, 10 residues, 1 model selected
> show sel atoms
> color sel red
> size #2:HOH stickRadius -0.2
Changed 0 bond radii
> name frozen radius sel
> select radius
10 atoms, 10 residues, 1 model selected
> ui tool show "Selection Inspector"
> size sel atomRadius 1.26
Changed 10 atom radii
> size sel atomRadius 1.2
Changed 10 atom radii
> size sel atomRadius 1.18
Changed 10 atom radii
> size sel atomRadius 1.16
Changed 10 atom radii
> select clear
> select #2:MG
2 atoms, 2 residues, 1 model selected
> ui tool show "Selection Inspector"
> size sel atomRadius 0.47
Changed 2 atom radii
> size sel atomRadius 0.4
Changed 2 atom radii
> select clear
> save /Users/angela/Desktop/Structure/Ab_7z9c_.cxs
> lighting full
[Repeated 2 time(s)]
> lighting soft
> lighting simple
> lighting soft
> lighting full
> select #1/D:513
8 atoms, 7 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
6 hydrogen bonds found
> hide #3 models
> ui tool show Distances
Exactly two atoms must be selected!
> select #1/D:513,#2/MG
Expected an objects specifier or a keyword
> select #1/D:513, #2/B:MG
Expected an objects specifier or a keyword
> select #1/D:513 #2/B:MG
9 atoms, 7 bonds, 2 residues, 2 models selected
Exactly two atoms must be selected!
> select #1/D:513 OD2 #2/B:MG
Expected a keyword
> select #1/D:513-OD2 #2/B:MG
1088 atoms, 1056 bonds, 139 residues, 2 models selected
> select #1/D:513:OD2 #2/B:MG
9 atoms, 7 bonds, 2 residues, 2 models selected
> select #1/D:513,OD2 #2/B:MG
9 atoms, 7 bonds, 2 residues, 2 models selected
> select clear
> select add #1/D:513@OD2
1 atom, 1 residue, 1 model selected
> select #2/B:901@MG
1 atom, 1 residue, 1 model selected
> select add #1/D:513@OD2
2 atoms, 2 residues, 2 models selected
> distance #2/B:901@MG #1/D:513@OD2
Distance between 7z9c #2/B MG 901 MG and 2024 Gyrase_last-coot7_NH.pdb #1/D
ASP 513 OD2: 1.874Å
> save /Users/angela/Desktop/Structure/AB_7z9c_Asp_dist.png width 2000 height
> 1151 supersample 3 transparentBackground true
> select clear
> open 5cdq
5cdq title:
2.95A structure of Moxifloxacin with S.aureus DNA gyrase and DNA [more
info...]
Chain information for 5cdq #5
---
Chain | Description | UniProt
A C R T | DNA gyrase subunit A | GYRA_STAAN 10-490
B D S U | DNA gyrase subunit B,DNA gyrase subunit B | GYRB_STAAN 414-640
E F V W | DNA (5'-D(P*GP*AP*GP*CP*GP*TP*AP*T*GP*GP*CP*CP*AP*TP*AP*CP*GP*CP*TP*T)-3') |
Non-standard residues in 5cdq #5
---
GOL — glycerol (glycerin; propane-1,2,3-triol)
MFX —
1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic
acid (moxifloxacin)
MG — magnesium ion
5cdq mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
83 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #5
22990 atoms, 23170 bonds, 157 pseudobonds, 3096 residues, 4 models selected
> hide sel atoms
> show sel cartoons
> color sel gray
> select #5/MG
Nothing selected
> view
> select #5:MG
14 atoms, 14 residues, 1 model selected
> select #5:MG
14 atoms, 14 residues, 1 model selected
> show sel atoms
> color sel green
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
> hide #!2 models
> hide #!1 models
> hide #4.1 models
> hide #!4 models
> select ::name="HOH"
308 atoms, 308 residues, 2 models selected
> show sel & #!5 atoms
> style sel & #!5 sphere
Changed 298 atom styles
> color sel red
> color sel green
> size #5:HOH stickRadius -0.2
Changed 0 bond radii
> show #!2 models
> hide #!2 models
> select HOH
Expected an objects specifier or a keyword
> select #5:HOH
298 atoms, 298 residues, 1 model selected
> color sel red
> size #5:HOH stickRadius -0.2
Changed 0 bond radii
> size #5:HOH stickRadius -0.2
Changed 0 bond radii
> select waters, resn HOH
Expected an objects specifier or a keyword
> size #5:HOH atomRadius -0.2
Changed 298 atom radii
> size #5:HOH atomRadius -0.2
Changed 298 atom radii
> size #5:HOH atomRadius -0.1
Changed 298 atom radii
> size #5:HOH atomRadius -0.05
Changed 298 atom radii
> select #5:MG
14 atoms, 14 residues, 1 model selected
> size #5:HOH atomRadius -0.05
Changed 298 atom radii
> size #5:HOH atomRadius -0.05
Changed 298 atom radii
> size #5:HOH atomRadius -0.05
Changed 298 atom radii
> size #5:HOH atomRadius -0.05
Changed 298 atom radii
> size #5:HOH atomRadius -0.05
Changed 298 atom radii
> size #5:HOH atomRadius -0.05
Changed 298 atom radii
> size #5:HOH atomRadius -0.05
Changed 298 atom radii
> size #5:MG atomRadius +0.2
Changed 14 atom radii
> select clear
> select #5:Asp508
Nothing selected
> select #5:508
32 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 32 atom styles
> color sel byhetero
> select #5:510
32 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel byhetero
> style sel ball
Changed 32 atom styles
> select clear
> show #!1 models
> show #!2 models
> mmaker #5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2024 Gyrase_last-coot7_NH.pdb, chain B (#1) with 5cdq, chain C
(#5), sequence alignment score = 1636.6
RMSD between 404 pruned atom pairs is 0.884 angstroms; (across all 478 pairs:
1.624)
> hide #!2 models
> select ::name="MFX"
174 atoms, 198 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel cyan
> color sel byhetero
> select clear
> select ::name="MFX"
174 atoms, 198 bonds, 6 residues, 1 model selected
> style sel ball
Changed 174 atom styles
> select clear
> size #5:MG atomRadius -0.2
Changed 14 atom radii
> select #5:MG
14 atoms, 14 residues, 1 model selected
> color sel lime
> size #5:HOH atomRadius -0.2
Changed 298 atom radii
> size #5:HOH atomRadius -0.1
Changed 298 atom radii
> select clear
> select #5:510
32 atoms, 28 bonds, 4 residues, 1 model selected
> size stickRadius -0.2
Cannot reduce bond radius to <= 0
> undo
> select #5:510
32 atoms, 28 bonds, 4 residues, 1 model selected
> size stickRadius +0.2
Changed 51651 bond radii
> select clear
> select #5:508
32 atoms, 28 bonds, 4 residues, 1 model selected
> select #1:511
34 atoms, 30 bonds, 4 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 34 atom styles
> color sel byhetero
> color sel teal
> color sel byhetero
> select clear
> select #1:511
34 atoms, 30 bonds, 4 residues, 1 model selected
> style sel stick
Changed 34 atom styles
> select #1:513
32 atoms, 28 bonds, 4 residues, 1 model selected
> style sel stick
Changed 32 atom styles
> select #5:508
32 atoms, 28 bonds, 4 residues, 1 model selected
> style sel stick
Changed 32 atom styles
> select #5:510
32 atoms, 28 bonds, 4 residues, 1 model selected
> style sel stick
Changed 32 atom styles
> select clear
> select add #5/A:641@O
1 atom, 1 residue, 1 model selected
> select add #5/E:2219@O
2 atoms, 2 residues, 1 model selected
> select add #5/B:1114@O
3 atoms, 3 residues, 1 model selected
> select add #5/A:617@O
4 atoms, 4 residues, 1 model selected
> select add #5/A:615@O
5 atoms, 5 residues, 1 model selected
> select add #5/B:1113@O
6 atoms, 6 residues, 1 model selected
> select add #5/A:601@O
7 atoms, 7 residues, 1 model selected
> select add #5/E:2209@O
8 atoms, 8 residues, 1 model selected
> select add #5/F:2204@O
9 atoms, 9 residues, 1 model selected
> select add #5/F:2215@O
10 atoms, 10 residues, 1 model selected
> select add #5/F:2209@O
11 atoms, 11 residues, 1 model selected
> select add #5/F:2205@O
12 atoms, 12 residues, 1 model selected
> select add #5/A:616@O
13 atoms, 13 residues, 1 model selected
Drag select of 1 residues
> select subtract #5/B:582
Nothing selected
> select add #5/F:2205@O
1 atom, 1 residue, 1 model selected
> select add #5/A:617@O
2 atoms, 2 residues, 1 model selected
> select add #5/F:2215@O
3 atoms, 3 residues, 1 model selected
> select add #5/E:2209@O
4 atoms, 4 residues, 1 model selected
> select add #5/A:615@O
5 atoms, 5 residues, 1 model selected
> select add #5/A:641@O
6 atoms, 6 residues, 1 model selected
> select add #5/E:2219@O
7 atoms, 7 residues, 1 model selected
> select add #5/B:1109@O
8 atoms, 8 residues, 1 model selected
> select add #5/E:2203@O
9 atoms, 9 residues, 1 model selected
> select add #5/B:1113@O
10 atoms, 10 residues, 1 model selected
> select add #5/E:2202@O
11 atoms, 11 residues, 1 model selected
> select add #5/F:2204@O
12 atoms, 12 residues, 1 model selected
> select add #5/F:2209@O
13 atoms, 13 residues, 1 model selected
> select add #5/A:619@O
14 atoms, 14 residues, 1 model selected
> select add #5/A:616@O
15 atoms, 15 residues, 1 model selected
> select add #5/A:642@O
16 atoms, 16 residues, 1 model selected
> select add #5/A:608@O
17 atoms, 17 residues, 1 model selected
> select add #5/E:2216@O
18 atoms, 18 residues, 1 model selected
> select add #5/F:2211@O
19 atoms, 19 residues, 1 model selected
> select add #5/C:623@O
20 atoms, 20 residues, 1 model selected
> select add #5/F:2216@O
21 atoms, 21 residues, 1 model selected
> hide sel atoms
> select clear
> select add #1/D:513
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/D:512
13 atoms, 11 bonds, 2 residues, 1 model selected
> select add #1/D:511
21 atoms, 18 bonds, 3 residues, 1 model selected
> select add #1/D:510
28 atoms, 24 bonds, 4 residues, 1 model selected
> select add #5/B:510@CB
29 atoms, 24 bonds, 5 residues, 2 models selected
> select add #5/B:509
34 atoms, 29 bonds, 6 residues, 2 models selected
> select add #5/B:511
41 atoms, 35 bonds, 7 residues, 2 models selected
> select add #5/B:512
49 atoms, 42 bonds, 8 residues, 2 models selected
> select add #5/B:513
53 atoms, 45 bonds, 9 residues, 2 models selected
> select add #1/A:601@C6
54 atoms, 45 bonds, 10 residues, 2 models selected
> select add #5/B:1001@MG
55 atoms, 45 bonds, 11 residues, 2 models selected
> select add #5/B:1116@O
56 atoms, 45 bonds, 12 residues, 2 models selected
> select add #5/B:1111@O
57 atoms, 45 bonds, 13 residues, 2 models selected
> select add #5/E:2101@C12
58 atoms, 45 bonds, 14 residues, 2 models selected
> select subtract #1/A:601@C6
57 atoms, 46 bonds, 13 residues, 2 models selected
> select add #5/B:514
62 atoms, 50 bonds, 14 residues, 2 models selected
> select add #5/B:515
72 atoms, 60 bonds, 15 residues, 2 models selected
> select add #5/B:516
80 atoms, 67 bonds, 16 residues, 2 models selected
> select add #5/B:517
91 atoms, 77 bonds, 17 residues, 2 models selected
> select add #5/B:518
98 atoms, 83 bonds, 18 residues, 2 models selected
> select subtract #5/B:511
91 atoms, 81 bonds, 17 residues, 2 models selected
> select subtract #5/B:510
90 atoms, 77 bonds, 16 residues, 2 models selected
> select add #5/B:510
98 atoms, 84 bonds, 17 residues, 2 models selected
Drag select of 1 residues
> select add #5/B:513
98 atoms, 84 bonds, 17 residues, 2 models selected
> select add #5/B:1107@O
99 atoms, 84 bonds, 18 residues, 2 models selected
> select add #1/A:601@C6
100 atoms, 84 bonds, 19 residues, 2 models selected
> select add #1/A:601@C11
101 atoms, 84 bonds, 19 residues, 2 models selected
> select add #1/A:601@C12
102 atoms, 84 bonds, 19 residues, 2 models selected
> select add #1/A:601@C15
103 atoms, 84 bonds, 19 residues, 2 models selected
> select add #1/A:601@C18
104 atoms, 84 bonds, 19 residues, 2 models selected
> select add #1/A:601@C17
105 atoms, 84 bonds, 19 residues, 2 models selected
> select add #5/F:8
125 atoms, 105 bonds, 20 residues, 2 models selected
> select add #5/F:7
146 atoms, 128 bonds, 21 residues, 2 models selected
> select add #5/F:6
166 atoms, 149 bonds, 22 residues, 2 models selected
> select add #1/F:13
187 atoms, 172 bonds, 23 residues, 2 models selected
> select add #1/F:14
209 atoms, 196 bonds, 24 residues, 2 models selected
> select subtract #5/B:510
201 atoms, 189 bonds, 23 residues, 2 models selected
> select add #5/B:510
209 atoms, 196 bonds, 24 residues, 2 models selected
> select add #5/B:511
216 atoms, 202 bonds, 25 residues, 2 models selected
> select clear
> select add #5/B:1001@MG
1 atom, 1 residue, 1 model selected
> select add #5/B:508@CG
2 atoms, 1 bond, 2 residues, 2 models selected
Drag select of 14 atoms, 105 residues, 11 bonds, 5 pseudobonds
Drag select of 74 atoms, 241 residues, 64 bonds, 7 shapes, 7 pseudobonds
> select ~sel & ##selected
32770 atoms, 33245 bonds, 143 pseudobonds, 4267 residues, 6 models selected
> select ~sel & ##selected
2080 atoms, 2054 bonds, 19 pseudobonds, 271 residues, 6 models selected
> select up
2083 atoms, 2054 bonds, 19 pseudobonds, 271 residues, 6 models selected
> select down
2080 atoms, 2054 bonds, 19 pseudobonds, 271 residues, 6 models selected
> select ~sel & ##selected
32770 atoms, 33245 bonds, 148 pseudobonds, 4267 residues, 7 models selected
> select ~sel & ##selected
2080 atoms, 2054 bonds, 19 pseudobonds, 271 residues, 6 models selected
> select clear
> select add #5/B:1001@MG
1 atom, 1 residue, 1 model selected
> select add #1/D:513@CG
2 atoms, 2 residues, 2 models selected
> select add #5/B:508@CG
3 atoms, 3 residues, 2 models selected
Drag select of 102 atoms, 386 residues, 80 bonds, 7 shapes, 11 pseudobonds
> select up
3157 atoms, 3162 bonds, 11 pseudobonds, 412 residues, 3 models selected
> select down
3138 atoms, 80 bonds, 11 pseudobonds, 412 residues, 3 models selected
> select down
3138 atoms, 80 bonds, 11 pseudobonds, 412 residues, 3 models selected
> select down
3138 atoms, 80 bonds, 11 pseudobonds, 412 residues, 3 models selected
> select up
3157 atoms, 3162 bonds, 11 pseudobonds, 412 residues, 3 models selected
> select down
3138 atoms, 80 bonds, 11 pseudobonds, 412 residues, 3 models selected
> view sel
> select ~sel & ##selected
31712 atoms, 32155 bonds, 144 pseudobonds, 4126 residues, 6 models selected
> hide sel atoms
> show sel atoms
> undo
[Repeated 1 time(s)]
> select clear
> select add #5/B:1001@MG
1 atom, 1 residue, 1 model selected
Drag select of 92 atoms, 302 residues, 75 bonds, 1 shapes, 11 pseudobonds
> select clear
> lighting full
> lighting soft
> lighting simple
> select add #5/A:611@O
1 atom, 1 residue, 1 model selected
> select add #5/B:1106@O
2 atoms, 2 residues, 1 model selected
> select add #5/B:1119@O
3 atoms, 3 residues, 1 model selected
> select add #5/T:4632@O
4 atoms, 4 residues, 1 model selected
> select add #5/F:2206@O
5 atoms, 5 residues, 1 model selected
> select add #1/D:510
12 atoms, 6 bonds, 6 residues, 2 models selected
> select add #1/D:509
20 atoms, 13 bonds, 7 residues, 2 models selected
> select add #1/D:459
28 atoms, 20 bonds, 8 residues, 2 models selected
> select add #1/D:439
36 atoms, 27 bonds, 9 residues, 2 models selected
> select add #1/D:438
40 atoms, 30 bonds, 10 residues, 2 models selected
> select add #1/D:437
49 atoms, 38 bonds, 11 residues, 2 models selected
> select add #1/D:436
56 atoms, 44 bonds, 12 residues, 2 models selected
> select add #5/A:28
62 atoms, 49 bonds, 13 residues, 2 models selected
> select add #5/A:24
70 atoms, 56 bonds, 14 residues, 2 models selected
> select add #5/A:27
78 atoms, 63 bonds, 15 residues, 2 models selected
> select add #5/A:30
86 atoms, 70 bonds, 16 residues, 2 models selected
Drag select of 2 residues
> select add #5/A:32
111 atoms, 74 bonds, 19 residues, 2 models selected
> select add #5/T:4618@O
112 atoms, 74 bonds, 20 residues, 2 models selected
> select add #5/A:33
123 atoms, 84 bonds, 21 residues, 2 models selected
> select add #5/A:34
128 atoms, 88 bonds, 22 residues, 2 models selected
> select add #5/A:35
136 atoms, 95 bonds, 23 residues, 2 models selected
> select add #5/A:31
143 atoms, 101 bonds, 24 residues, 2 models selected
> select add #5/A:25
155 atoms, 113 bonds, 25 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select add #5/A:29
162 atoms, 119 bonds, 26 residues, 2 models selected
> select add #1/D:458
169 atoms, 126 bonds, 27 residues, 2 models selected
> select add #5/B:459
173 atoms, 129 bonds, 28 residues, 2 models selected
> select add #5/B:458
184 atoms, 139 bonds, 29 residues, 2 models selected
> hide sel cartoons
> select add #5/B:581
190 atoms, 144 bonds, 30 residues, 2 models selected
> select add #5/B:580
202 atoms, 156 bonds, 31 residues, 2 models selected
> select add #5/B:545
206 atoms, 159 bonds, 32 residues, 2 models selected
> select add #5/B:544
213 atoms, 165 bonds, 33 residues, 2 models selected
> select add #5/B:543
220 atoms, 172 bonds, 34 residues, 2 models selected
> select add #1/D:440
226 atoms, 177 bonds, 35 residues, 2 models selected
> select add #1/D:441
231 atoms, 181 bonds, 36 residues, 2 models selected
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select add #1/D:443
235 atoms, 184 bonds, 37 residues, 2 models selected
> hide sel cartoons
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select ::name="DA"::name="DC"::name="DG"::name="DT"
3689 atoms, 4125 bonds, 93 pseudobonds, 184 residues, 5 models selected
> nucleotides sel & #!1,5 tube/slab shape box
> show sel & #!1,5 atoms
> select clear
> select add #1/D:442
4 atoms, 3 bonds, 1 residue, 1 model selected
> hide sel cartoons
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select add #1/D:419
13 atoms, 11 bonds, 2 residues, 1 model selected
> select add #1/D:420
21 atoms, 18 bonds, 3 residues, 1 model selected
> select add #1/D:457
29 atoms, 25 bonds, 4 residues, 1 model selected
> select add #1/D:456
37 atoms, 32 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select clear
> select add #5/B:1114@O
1 atom, 1 residue, 1 model selected
> select add #5/F:2217@O
2 atoms, 2 residues, 1 model selected
> hide sel atoms
> select clear
> select add #5/B:1115@O
1 atom, 1 residue, 1 model selected
> select add #5/B:1103@O
2 atoms, 2 residues, 1 model selected
> select add #5/A:601@O
3 atoms, 3 residues, 1 model selected
> select add #5/E:2217@O
4 atoms, 4 residues, 1 model selected
> hide sel atoms
> select add #5/B:460
13 atoms, 8 bonds, 5 residues, 1 model selected
> hide sel cartoons
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select add #5/B:475
21 atoms, 15 bonds, 6 residues, 1 model selected
Drag select of 11 atoms, 8 residues, 4 bonds, 6 shapes
Drag select of 2 residues, 2 pseudobonds
> select clear
> select add #5/B:1001@MG
1 atom, 1 residue, 1 model selected
Drag select of 37 atoms, 158 residues, 6 pseudobonds, 25 bonds, 14 shapes
> select clear
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select add #1/D:462
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #1/D:461
13 atoms, 11 bonds, 2 residues, 1 model selected
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select add #1/D:460
22 atoms, 19 bonds, 3 residues, 1 model selected
> hide sel cartoons
> select add #1/D:479
31 atoms, 27 bonds, 4 residues, 1 model selected
> select add #1/D:480
38 atoms, 33 bonds, 5 residues, 1 model selected
> select add #1/D:482
45 atoms, 39 bonds, 6 residues, 1 model selected
> hide sel cartoons
> select add #1/D:478
54 atoms, 47 bonds, 7 residues, 1 model selected
> select add #1/D:481
58 atoms, 50 bonds, 8 residues, 1 model selected
> hide sel cartoons
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select add #5/B:463
66 atoms, 57 bonds, 9 residues, 2 models selected
> select add #5/B:462
74 atoms, 64 bonds, 10 residues, 2 models selected
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select add #5/B:461
82 atoms, 71 bonds, 11 residues, 2 models selected
> hide sel cartoons
> select ::name="MFX"
174 atoms, 198 bonds, 6 residues, 1 model selected
> color sel cadet blue
> color sel byhetero
> select clear
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select add #5/B:1117@O
1 atom, 1 residue, 1 model selected
> select add #5/E:2208@O
2 atoms, 2 residues, 1 model selected
> select add #5/F:2212@O
3 atoms, 3 residues, 1 model selected
> select add #5/F:2102@MG
4 atoms, 4 residues, 1 model selected
> select add #5/F:2103@O02
5 atoms, 5 residues, 1 model selected
> select add #5/F:2103@O
6 atoms, 5 residues, 1 model selected
> hide sel atoms
> color #5 black
> undo
> hide #5.3 models
> show #5.3 models
> hide #5.2 models
> show #5.2 models
> color #5.2 black models
> color #5.2 #fffb00ff models
> color #5.2 #ff9a2aff models
> color #5.2 #fdb22fff models
> color #5.2 #f2cd34ff models
> color #5.2 #ffca33ff models
> color #5.2 #ffaf2eff models
> select add #5/B:582
10 atoms, 3 bonds, 6 residues, 1 model selected
> select add #5/B:583
18 atoms, 10 bonds, 7 residues, 1 model selected
> hide sel cartoons
> select clear
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select add #5/E:2204@O
1 atom, 1 residue, 1 model selected
> hide sel atoms
> select clear
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select nucleic-acid
3689 atoms, 4125 bonds, 93 pseudobonds, 184 residues, 5 models selected
> select clear
> select #5/E/F
907 atoms, 972 bonds, 51 pseudobonds, 82 residues, 4 models selected
> color sel gainsboro
> color #5.2 #fed635ff models
> color #5.2 #f56522ff models
> color #5.2 #ff962aff models
> color #5.2 #ff8126ff models
> color #5.2 #fd7023ff models
> color #5.2 #0f0914ff models
> color #5.2 #cf8227ff models
> nucleotides sel stubs
> nucleotides sel tube/slab shape box
> nucleotides sel ladder
> select #1/E/F/G/H
821 atoms, 917 bonds, 40 residues, 1 model selected
> nucleotides sel ladder
> nucleotides sel tube/slab shape box
[Repeated 1 time(s)]
> nucleotides sel ladder
> select clear
> select ::name="MFX"
174 atoms, 198 bonds, 6 residues, 1 model selected
> color sel cadet blue
> color sel byhetero
> select #1/E/F/G/H
821 atoms, 917 bonds, 40 residues, 1 model selected
> color sel goldenrod
[Repeated 1 time(s)]
> lighting full
> select clear
> lighting simple
> select add #5/F:2214@O
1 atom, 1 residue, 1 model selected
> select add #5/E:2206@O
2 atoms, 2 residues, 1 model selected
> select add #5/E:2210@O
3 atoms, 3 residues, 1 model selected
> select add #5/E:2211@O
4 atoms, 4 residues, 1 model selected
> color sel red
> select clear
> select add #5/F:2103@C17
1 atom, 1 residue, 1 model selected
> select subtract #5/F:2103@C17
Nothing selected
> select add #5/E:2206@O
1 atom, 1 residue, 1 model selected
> select add #5/E:2210@O
2 atoms, 2 residues, 1 model selected
> select add #5/B:1104@O
3 atoms, 3 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select clear
> select add #5/B:584
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #5/B:585
13 atoms, 11 bonds, 2 residues, 1 model selected
> select add #5/B:586
21 atoms, 18 bonds, 3 residues, 1 model selected
> select add #5/B:587
29 atoms, 25 bonds, 4 residues, 1 model selected
> select add #5/B:435
38 atoms, 33 bonds, 5 residues, 1 model selected
> select add #5/B:436
42 atoms, 36 bonds, 6 residues, 1 model selected
> hide sel cartoons
> select add #5/B:437
50 atoms, 43 bonds, 7 residues, 1 model selected
> select add #5/B:457
58 atoms, 50 bonds, 8 residues, 1 model selected
> hide sel cartoons
> select add #1/D:765
66 atoms, 57 bonds, 9 residues, 2 models selected
> hide sel cartoons
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select add #1/D:511
74 atoms, 64 bonds, 10 residues, 2 models selected
> select ~sel & ##selected
34776 atoms, 35230 bonds, 162 pseudobonds, 4522 residues, 7 models selected
> select clear
> select #1:509-510
56 atoms, 52 bonds, 8 residues, 1 model selected
> show sel cartoons
> select clear
> select add #5/B:626
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #5/A:22
18 atoms, 17 bonds, 2 residues, 1 model selected
> select add #5/B:624
26 atoms, 24 bonds, 3 residues, 1 model selected
> select add #5/B:542
33 atoms, 31 bonds, 4 residues, 1 model selected
> select add #5/B:541
42 atoms, 39 bonds, 5 residues, 1 model selected
> hide sel cartoons
> select add #5/B:625
49 atoms, 45 bonds, 6 residues, 1 model selected
> hide sel cartoons
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> color #5.2 #160711ff models
> color #5.2 #cea62dff models
> color #5.2 #d67325ff models
> select #5/E/F
907 atoms, 972 bonds, 51 pseudobonds, 82 residues, 4 models selected
> color sel slate gray
> lighting full
> lighting simple
> color sel silver
> color sel tan
> color sel olive
> color sel peru
> color sel sadle brown
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> lighting full
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting simple
> color sel alice blue
> color sel mint cream
> color sel lavender
> color sel thistle
> color sel light steel blue
> color sel dark khaki
> color sel dark olive green
> color sel darkred see green
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel dark sea green
> color sel cadet blue
> select #1:510
24 atoms, 20 bonds, 4 residues, 1 model selected
> select #1:513
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel blue
> color sel byhetero
> select #1:511
34 atoms, 30 bonds, 4 residues, 1 model selected
> color sel blue
> color sel byhetero
> select clear
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select #5:2103
58 atoms, 66 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #5:2101
116 atoms, 132 bonds, 4 residues, 1 model selected
> color sel byhetero
> select clear
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select add #5/F:2210@O
1 atom, 1 residue, 1 model selected
> select add #1/D:477
7 atoms, 5 bonds, 2 residues, 2 models selected
> select add #1/D:476
13 atoms, 10 bonds, 3 residues, 2 models selected
> select add #1/D:475
21 atoms, 17 bonds, 4 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select clear
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select add #5/E:2207@O
1 atom, 1 residue, 1 model selected
> select add #5/B:1105@O
2 atoms, 2 residues, 1 model selected
> hide sel atoms
> save /Users/angela/Desktop/Structure/Ab_5cdq_Asp.png width 2000 height 1151
> supersample 3 transparentBackground true
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> save /Users/angela/Desktop/Structure/Ab_Asps.cxs
> show #!2 models
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> hide #5.3 models
> hide #5.2 models
> hide #5.1 models
> hide #!5 models
> show #4.1 models
> show #3 models
> hide #4.1 models
> hide #!4 models
> hide #3 models
> select #2:500
34 atoms, 30 bonds, 4 residues, 1 model selected
> style sel stick
Changed 34 atom styles
> select #2:B:HOH
10 atoms, 10 residues, 1 model selected
> color sel red
> size #2/B:HOH atomRadius -0.2
Changed 4 atom radii
> size #2/B:HOH atomRadius -0.1
Changed 4 atom radii
> select add #2/B:731
21 atoms, 10 bonds, 11 residues, 1 model selected
> select add #2/B:732
32 atoms, 20 bonds, 12 residues, 1 model selected
> select subtract #2/B:732
21 atoms, 10 bonds, 11 residues, 1 model selected
> select add #1/D:464
29 atoms, 17 bonds, 12 residues, 2 models selected
> select add #1/D:463
37 atoms, 24 bonds, 13 residues, 2 models selected
> select add #2/B:449
46 atoms, 32 bonds, 14 residues, 2 models selected
> select add #2/B:448
50 atoms, 35 bonds, 15 residues, 2 models selected
> hide sel cartoons
> select add #2/B:450
58 atoms, 42 bonds, 16 residues, 2 models selected
> select add #2/B:451
66 atoms, 49 bonds, 17 residues, 2 models selected
> hide sel cartoons
> select add #2/B:737
75 atoms, 57 bonds, 18 residues, 2 models selected
> select add #2/B:738
86 atoms, 67 bonds, 19 residues, 2 models selected
> select add #2/B:735
92 atoms, 72 bonds, 20 residues, 2 models selected
> select add #2/B:734
100 atoms, 79 bonds, 21 residues, 2 models selected
> select add #2/B:733
104 atoms, 82 bonds, 22 residues, 2 models selected
> select add #2/B:732
115 atoms, 92 bonds, 23 residues, 2 models selected
> hide sel cartoons
> select add #2/B:736
123 atoms, 99 bonds, 24 residues, 2 models selected
> hide sel cartoons
> select add #2/B:739
135 atoms, 111 bonds, 25 residues, 2 models selected
> select add #2/B:740
144 atoms, 119 bonds, 26 residues, 2 models selected
> select add #2/B:741
148 atoms, 122 bonds, 27 residues, 2 models selected
> hide sel cartoons
> select clear
> color #2.2 #df7e26ff models
> color #2.2 #dd8728ff models
> color #2.2 #dc8a28ff models
> save /Users/angela/Desktop/Structure/Ab_7z9c_Aspb.png width 2000 height 1151
> supersample 3 transparentBackground true
> color #2.2 #ff9300ff models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> save /Users/angela/Desktop/Structure/Ab_Asps.cxs
——— End of log from Tue Jul 29 16:24:33 2025 ———
opened ChimeraX session
> open /Users/angela/Desktop/Structure/2024_Gyrase_last-coot-11.pdb
Chain information for 2024_Gyrase_last-coot-11.pdb #6
---
Chain | Description
A | No description available
B | No description available
C D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
> hide #!2 models
> hide #!1 models
> hide #!6 atoms
> show #!6 cartoons
> select #6/A/B
16370 atoms, 16501 bonds, 2 pseudobonds, 1038 residues, 2 models selected
> dssp
> select #6/C/D
5660 atoms, 5702 bonds, 2 pseudobonds, 358 residues, 2 models selected
> color sel dark slate blue
> select #6/E/F/G/H
1276 atoms, 1372 bonds, 40 residues, 1 model selected
> nucleotides sel tube/slab shape box
> show sel atoms
> nucleotides sel slab
> style nucleic & sel stick
Changed 1276 atom styles
> nucleotides sel tube/slab shape ellipsoid
> nucleotides sel tube/slab shape muffler
> nucleotides sel stubs
> color sel godenrod
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel goldenrod
> select #6/A/B
16370 atoms, 16501 bonds, 2 pseudobonds, 1038 residues, 2 models selected
> color sel bisque
> select #6/A:DK4
58 atoms, 63 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel ball
Changed 58 atom styles
> color sel orangered
> color sel byhetero
> show #!2 models
> select ~sel & ##selected
23248 atoms, 23512 bonds, 4 pseudobonds, 1435 residues, 2 models selected
> select ~sel & ##selected
58 atoms, 63 bonds, 1 residue, 1 model selected
> mmaker #2 to #6 showAlignment true
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2024_Gyrase_last-coot-11.pdb, chain B (#6) with 7z9c, chain A (#2),
sequence alignment score = 1973.9
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7z9c #2/A, 2024_Gyrase_last-
coot-11.pdb #6/B
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 444 pruned atom pairs is 0.958 angstroms; (across all 514 pairs:
1.590)
> show #!1 models
> hide #!6 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!6 models
> color #2/A/B/C/D pink
> select ::name="BWH"
62 atoms, 66 bonds, 1 residue, 1 model selected
> color sel gray
> color sel byhetero
> select clear
> select #2/E/F/G/H
1306 atoms, 1460 bonds, 66 residues, 1 model selected
> nucleotides sel stubs
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select #2/D:498,500
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 16 atom styles
> color sel byhetero
> select #6/D:511,513
24 atoms, 22 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 24 atom styles
> color sel byhetero
> ui tool show Matchmaker
> matchmaker #!2 to #6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2024_Gyrase_last-coot-11.pdb, chain B (#6) with 7z9c, chain A (#2),
sequence alignment score = 1973.9
RMSD between 444 pruned atom pairs is 0.958 angstroms; (across all 514 pairs:
1.590)
> ui tool show Matchmaker
> matchmaker #!2 & sel to #6 & sel alg Smith-Waterman
No molecules/chains to match specified
> select clear
> ui tool show Matchmaker
> mmaker #6 to #2/a pair bs alg sw matrix PAM-150 ss false cut 5.0
Parameters
---
Chain pairing | bs
Alignment algorithm | Smith-Waterman
Similarity matrix | PAM-150
No secondary-structure guidance used
Gap open | 12
Gap extend | 1
Iteration cutoff | 5
Matchmaker 7z9c (#2) with 2024_Gyrase_last-coot-11.pdb (#6), sequence
alignment score = 1707
RMSD between 506 pruned atom pairs is 1.366 angstroms; (across all 514 pairs:
1.583)
> mmaker #6/a,C to #2/a,b pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7z9c, chain A (#2) with 2024_Gyrase_last-coot-11.pdb, chain A (#6),
sequence alignment score = 1959.3
Matchmaker 7z9c, chain B (#2) with 2024_Gyrase_last-coot-11.pdb, chain C (#6),
sequence alignment score = 581.8
RMSD between 404 pruned atom pairs is 0.910 angstroms; (across all 682 pairs:
31.157)
> select #2/D:498,500
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #2/B:498,500
16 atoms, 14 bonds, 2 residues, 1 model selected
> color sel byhetero
> show sel atoms
> style sel stick
Changed 16 atom styles
> select #2/B:MG
1 atom, 1 residue, 1 model selected
> color sel lime green
> select #2/C:HOH
1 atom, 1 residue, 1 model selected
> color sel red
> style sel sphere
Changed 1 atom style
> size sel atomRadius -0.2
Changed 1 atom radii
> size sel atomRadius -0.4
Changed 1 atom radii
> size sel atomRadius -0.2
Changed 1 atom radii
> size sel atomRadius -0.1
Changed 1 atom radii
> size sel atomRadius -0.1
Changed 1 atom radii
> size sel atomRadius +0.1
Changed 1 atom radii
> size sel atomRadius -0.05
Changed 1 atom radii
> select #2/B:HOH
4 atoms, 4 residues, 1 model selected
> color sel red
> select #6/D:511,513
24 atoms, 22 bonds, 2 residues, 1 model selected
> color #2.2 #797979ff models
> color #2.2 #5e5e5eff models
> delete sel hydrogen
Expected a keyword
> delete sel hydrogens
Expected a keyword
> delete sel H
Expected a keyword
> delete sel Hydrogen
Expected a keyword
> delete sel Hydrogens
Expected a keyword
> delete Hydrogens
Missing or invalid "atoms" argument: invalid atoms specifier
> delete Hydrogen
Missing or invalid "atoms" argument: invalid atoms specifier
> delete H
> select clear
> select add #6/A:72
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2/A:74
16 atoms, 14 bonds, 2 residues, 2 models selected
> select add #6/A:73
20 atoms, 17 bonds, 3 residues, 2 models selected
> select add #6/A:74
29 atoms, 25 bonds, 4 residues, 2 models selected
> select add #2/A:75
33 atoms, 28 bonds, 5 residues, 2 models selected
> select add #2/A:77
45 atoms, 40 bonds, 6 residues, 2 models selected
> select add #6/A:76
55 atoms, 50 bonds, 7 residues, 2 models selected
> select add #6/A:75
67 atoms, 62 bonds, 8 residues, 2 models selected
> select add #2/A:54
74 atoms, 68 bonds, 9 residues, 2 models selected
> select add #6/A:77
81 atoms, 75 bonds, 10 residues, 2 models selected
> select add #6/A:53
89 atoms, 82 bonds, 11 residues, 2 models selected
> select add #6/A:78
99 atoms, 92 bonds, 12 residues, 2 models selected
> select add #2/A:55
107 atoms, 99 bonds, 13 residues, 2 models selected
> hide sel cartoons
> select add #2/A:76
116 atoms, 107 bonds, 14 residues, 2 models selected
> select add #2/A:78
126 atoms, 117 bonds, 15 residues, 2 models selected
> select add #2/A:79
133 atoms, 124 bonds, 16 residues, 2 models selected
> select add #2/A:80
143 atoms, 134 bonds, 17 residues, 2 models selected
> hide sel cartoons
> select add #6/A:52
152 atoms, 142 bonds, 18 residues, 2 models selected
> hide sel cartoons
> select add #2/A:73
159 atoms, 148 bonds, 19 residues, 2 models selected
> select add #6/A:71
166 atoms, 154 bonds, 20 residues, 2 models selected
> select add #2/A:72
174 atoms, 161 bonds, 21 residues, 2 models selected
> select add #6/A:70
182 atoms, 168 bonds, 22 residues, 2 models selected
> hide sel cartoons
> select add #2/A:56
186 atoms, 171 bonds, 23 residues, 2 models selected
> select add #6/A:54
190 atoms, 174 bonds, 24 residues, 2 models selected
> hide sel cartoons
> select add #2/B:521
198 atoms, 181 bonds, 25 residues, 2 models selected
> select add #6/D:534
206 atoms, 188 bonds, 26 residues, 2 models selected
> select add #2/B:522
213 atoms, 194 bonds, 27 residues, 2 models selected
> select add #6/D:535
220 atoms, 200 bonds, 28 residues, 2 models selected
> select add #2/B:520
229 atoms, 208 bonds, 29 residues, 2 models selected
> hide sel cartoons
> select add #6/D:533
238 atoms, 216 bonds, 30 residues, 2 models selected
> hide sel cartoons
> select add #2/A:150
246 atoms, 223 bonds, 31 residues, 2 models selected
> select add #2/A:151
250 atoms, 226 bonds, 32 residues, 2 models selected
> select add #2/A:149
262 atoms, 238 bonds, 33 residues, 2 models selected
> select add #6/A:147
274 atoms, 250 bonds, 34 residues, 2 models selected
> select add #6/A:148
282 atoms, 257 bonds, 35 residues, 2 models selected
> select add #6/A:146
290 atoms, 264 bonds, 36 residues, 2 models selected
> select add #2/A:148
298 atoms, 271 bonds, 37 residues, 2 models selected
> select add #6/A:145
306 atoms, 278 bonds, 38 residues, 2 models selected
> select add #2/A:147
314 atoms, 285 bonds, 39 residues, 2 models selected
> select add #6/A:149
318 atoms, 288 bonds, 40 residues, 2 models selected
> hide sel cartoons
> select add #2/A:152
325 atoms, 294 bonds, 41 residues, 2 models selected
> select add #6/A:150
331 atoms, 299 bonds, 42 residues, 2 models selected
> select add #2/A:153
340 atoms, 307 bonds, 43 residues, 2 models selected
> select add #6/A:152
351 atoms, 317 bonds, 44 residues, 2 models selected
> select add #6/A:151
360 atoms, 325 bonds, 45 residues, 2 models selected
> hide sel cartoons
> select add #2/A:154
369 atoms, 333 bonds, 46 residues, 2 models selected
> hide sel cartoons
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting simple
> ui tool show Distances
> select add #6/D:513@OD2
370 atoms, 333 bonds, 47 residues, 2 models selected
> select add #2/B:901@MG
371 atoms, 333 bonds, 48 residues, 2 models selected
Exactly two atoms must be selected!
[Repeated 1 time(s)]
> select clear
> select add #2/B:901@MG
1 atom, 1 residue, 1 model selected
> select add #6/D:513@OD2
2 atoms, 2 residues, 2 models selected
> distance #2/B:901@MG #6/D:513@OD2
Distance between 7z9c #2/B MG 901 MG and 2024_Gyrase_last-coot-11.pdb #6/D ASP
513 OD2: 1.968Å
> select clear
> save "/Users/angela/Desktop/Hannover/Results/Cryo/Paper/Final
> Images/Ab_Eco_Asp.png" width 2000 height 1315 supersample 3
> transparentBackground true
> show #!5 models
> hide #2.2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> show #5.1 models
> show #5.2 models
> show #5.3 models
> hide #5.3 models
> show #5.3 models
> hide #5.3 models
> show #5.3 models
> color #5.2 #5e5e5eff models
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> save /Users/angela/Desktop/Structure/Ab_Asps.cxs
——— End of log from Wed Aug 13 11:08:38 2025 ———
opened ChimeraX session
> show #!2 models
> hide #!5 models
> hide #!6 models
> show #!6 models
> select #6/D:511,513
16 atoms, 14 bonds, 2 residues, 1 model selected
> color sel medium blue
> color sel byhetero
> color sel dark blue
> color sel byhetero
> color sel blue
> color sel byhetero
> color sel medium blue
> color sel byhetero
> show #2.2 models
> show #3 models
> show #!4 models
> hide #!4 models
> select clear
> ui tool show Distances
Exactly two atoms must be selected!
> select add #6/D:511@OD2
1 atom, 1 residue, 1 model selected
> select add #2/B:901@MG
2 atoms, 2 residues, 2 models selected
> distance #6/D:511@OD2 #2/B:901@MG
Distance between 2024_Gyrase_last-coot-11.pdb #6/D ASP 511 OD2 and 7z9c #2/B
MG 901 MG: 3.306Å
> select clear
> save "/Users/angela/Desktop/Hannover/Results/Cryo/Paper/Final
> Images/Ab_7z9c_Asp.png" width 2000 height 1315 supersample 3
> transparentBackground true
> show #!5 models
> hide #!2 models
> hide #2.2 models
> hide #3 models
> color #6 turquoise
> color #6 medium turquoise
> undo
[Repeated 1 time(s)]
> color #5 medium turquoise
> color #5 light sea green
> color #5 medium aquamarine
> color #5 light sea green
> color #5 dark cyan
> color #5 light sea green
> color #5 dark cyan
> color #5 light sea green
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select #5/D:508,510
16 atoms, 14 bonds, 2 residues, 1 model selected
> color sel byhetero
> select #5/D:MG
1 atom, 1 residue, 1 model selected
> color sel lime green
> select #5/D:HOH
5 atoms, 5 residues, 1 model selected
> color sel red
> color #5 #5e5e5eff
> undo
> color #5.2 #5e5e5eff models
> select #5/F:MFX
58 atoms, 66 bonds, 2 residues, 1 model selected
> color sel olive
> color sel byhetero
> select clear
> ui tool show Matchmaker
> matchmaker #!5 to #6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2024_Gyrase_last-coot-11.pdb, chain B (#6) with 5cdq, chain C (#5),
sequence alignment score = 1647.4
RMSD between 404 pruned atom pairs is 0.883 angstroms; (across all 478 pairs:
1.624)
> mmaker #5/a,b to #2/c,d pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 7z9c, chain C (#2) with 5cdq, chain A (#5), sequence alignment
score = 1702.9
Matchmaker 7z9c, chain D (#2) with 5cdq, chain B (#5), sequence alignment
score = 447.9
RMSD between 455 pruned atom pairs is 1.293 angstroms; (across all 670 pairs:
3.004)
> mmaker #5/a,b to #6/c,d pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2024_Gyrase_last-coot-11.pdb, chain C (#6) with 5cdq, chain A (#5),
sequence alignment score = 47.8
Matchmaker 2024_Gyrase_last-coot-11.pdb, chain D (#6) with 5cdq, chain B (#5),
sequence alignment score = 617.6
RMSD between 144 pruned atom pairs is 0.840 angstroms; (across all 315 pairs:
37.448)
> select #5/B:HOH
21 atoms, 21 residues, 1 model selected
> color sel red
> select #5/B:MG
1 atom, 1 residue, 1 model selected
> color sel lime green
> select #5/E:MFX
29 atoms, 33 bonds, 1 residue, 1 model selected
> color sel olive
> color sel byhetero
> select clear
> ui tool show Distances
Exactly two atoms must be selected!
> select add #6/D:513@OD2
1 atom, 1 residue, 1 model selected
> select add #5/B:1001@MG
2 atoms, 2 residues, 2 models selected
> distance #6/D:513@OD2 #5/B:1001@MG
Distance between 2024_Gyrase_last-coot-11.pdb #6/D ASP 513 OD2 and 5cdq #5/B
MG 1001 MG: 2.389Å
> select add #6/D:511@OD2
3 atoms, 3 residues, 2 models selected
> select subtract #6/D:513@OD2
2 atoms, 2 residues, 2 models selected
> distance #5/B:1001@MG #6/D:511@OD2
Distance between 5cdq #5/B MG 1001 MG and 2024_Gyrase_last-coot-11.pdb #6/D
ASP 511 OD2: 3.250Å
> mmaker #5/a,b to #6/a,c pair ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2024_Gyrase_last-coot-11.pdb, chain A (#6) with 5cdq, chain A (#5),
sequence alignment score = 1645.2
Matchmaker 2024_Gyrase_last-coot-11.pdb, chain C (#6) with 5cdq, chain B (#5),
sequence alignment score = 630.8
RMSD between 361 pruned atom pairs is 0.872 angstroms; (across all 653 pairs:
32.121)
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select clear
> ui tool show Distances
> select add #6/D:513@OD2
1 atom, 1 residue, 1 model selected
> select add #5/B:1001@MG
2 atoms, 2 residues, 2 models selected
> distance #6/D:513@OD2 #5/B:1001@MG
Distance already exists; modify distance properties with 'distance style'
> select subtract #6/D:513@OD2
1 atom, 1 residue, 1 model selected
> select subtract #5/B:1001@MG
Nothing selected
> select add #5/B:1001@MG
1 atom, 1 residue, 1 model selected
> select add #6/D:513@OD2
2 atoms, 2 residues, 2 models selected
> distance #5/B:1001@MG #6/D:513@OD2
Distance already exists; modify distance properties with 'distance style'
> ~distance #6/D:513@OD2 #5/B:1001@MG
> ~distance #5/B:1001@MG #6/D:511@OD2
> distance #5/B:1001@MG #6/D:513@OD2
Distance between 5cdq #5/B MG 1001 MG and 2024_Gyrase_last-coot-11.pdb #6/D
ASP 513 OD2: 2.275Å
> distance #5/B:1001@MG #6/D:513@OD2
Distance already exists; modify distance properties with 'distance style'
> select subtract #6/D:513@OD2
1 atom, 1 residue, 1 model selected
> select add #6/D:511@OD2
2 atoms, 2 residues, 2 models selected
> distance #5/B:1001@MG #6/D:511@OD2
Distance between 5cdq #5/B MG 1001 MG and 2024_Gyrase_last-coot-11.pdb #6/D
ASP 511 OD2: 4.165Å
> show #!2 models
> hide #!5 models
> hide #5.1 models
> hide #5.2 models
> hide #5.3 models
> mmaker #6/a,b to #6/a,c pair ss
Different number of reference/match chains (1 ref, 2 match)
> select add #2/B:901@MG
3 atoms, 3 residues, 3 models selected
> hbonds sel & #!2,6 reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 5cdq #5/W DT 2020 O4'; 5cdq #5/U ARG 458 NE; 5cdq #5/R ARG 252
NE
3 hydrogen bonds found
> show #!5 models
> hide #!2 models
> select #5/B:583
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show sel cartoons
> show #5.2 models
> show #5.3 models
> hide #!5 models
> hide #5.2 models
> hide #5.3 models
> show #!2 models
> show #3 models
> show #!4 models
> hide #!4 models
> hide #3 models
> select #2/B:MG
1 atom, 1 residue, 1 model selected
> hbonds sel reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 5cdq #5/W DT 2020 O4'; 5cdq #5/U ARG 458 NE; 5cdq #5/R ARG 252
NE
0 hydrogen bonds found
> hide #!6 models
> save /Users/angela/Desktop/Ab_test.cxs
——— End of log from Wed Aug 13 11:43:29 2025 ———
opened ChimeraX session
> select clear
> select #2/B:MG
1 atom, 1 residue, 1 model selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> ui mousemode right distance
> select add #2/B:1004@O
2 atoms, 2 residues, 1 model selected
> select subtract #2/B:901@MG
1 atom, 1 residue, 1 model selected
> select add #2/B:1002@O
2 atoms, 2 residues, 1 model selected
> select add #2/B:1003@O
3 atoms, 3 residues, 1 model selected
> select add #2/B:1001@O
4 atoms, 4 residues, 1 model selected
> select add #2/C:1001@O
5 atoms, 5 residues, 1 model selected
> ui mousemode right distance
> select add #2/B:901@MG
6 atoms, 6 residues, 1 model selected
> select subtract #2/B:1004@O
5 atoms, 5 residues, 1 model selected
> select clear
> show #!6 models
> select #6/E/F/G/H
821 atoms, 917 bonds, 40 residues, 1 model selected
> color sel dark goldenrod
> color sel goldenrod
> color sel dark goldenrod
> select clear
> hide #!6 models
> show #!6 models
> show #3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> preset "initial styles" "original look"
Using preset: Initial Styles / Original Look
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!6 models
> color #2 pink
> show #!5 models
> hide #!2,5-6 atoms
> show #!2,5-6 cartoons
> select #6/E/F/G/H
821 atoms, 917 bonds, 40 residues, 1 model selected
> color sel dark goldenrod
> nucleotides sel stubs
> show sel atoms
> select #6/A/B
8201 atoms, 8332 bonds, 2 pseudobonds, 1038 residues, 2 models selected
> color sel bisque
> dssp
> select #6/C/D
2838 atoms, 2880 bonds, 2 pseudobonds, 358 residues, 2 models selected
> color sel dark slate blue
> select #5
22990 atoms, 23170 bonds, 68 pseudobonds, 3096 residues, 3 models selected
> color sel medium turquoise
> hide #!5 models
> select #6/A:DK4
58 atoms, 63 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel orange red
> color sel orangered
> style sel ball
Changed 58 atom styles
> color sel byhetero
> select #2/BWH
Nothing selected
> show #!2,6 atoms
> undo
> select ::name="BWH"
62 atoms, 66 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel grey
> style sel ball
Changed 62 atom styles
> color sel byhetero
> select ::name="HOH"
308 atoms, 308 residues, 2 models selected
> show sel & #!2 atoms
> color sel red
> select ::name="MG"
16 atoms, 16 residues, 2 models selected
> color sel lime green
> show sel & #!2 atoms
> select #2/B:598,500
17 atoms, 15 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 17 atom styles
> select #2/B:498,500
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 16 atom styles
> color sel byhetero
> select clear
> select #2/B:MG
1 atom, 1 residue, 1 model selected
> hbonds sel reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 5cdq #5/W DT 2020 O4'; 5cdq #5/U ARG 458 NE; 5cdq #5/R ARG 252
NE
0 hydrogen bonds found
> select #6/B:511,513
17 atoms, 15 bonds, 2 residues, 1 model selected
> select #6/D:511,513
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 16 atom styles
> color sel byhetero
> color sel medium blue
> color sel dark blue
> color sel medium blue
> color sel byhetero
> select clear
> ui tool show Distances
> select add #6/D:511@OD2
1 atom, 1 residue, 1 model selected
> select add #2/B:901@MG
2 atoms, 2 residues, 2 models selected
> distance #6/D:511@OD2 #2/B:901@MG
Distance already exists; modify distance properties with 'distance style'
> ~distance #2/B:901@MG #1/D:513@OD2
> ~distance #2/B:901@MG #6/D:513@OD2
> ~distance #6/D:511@OD2 #2/B:901@MG
> distance #6/D:511@OD2 #2/B:901@MG
Distance between 2024_Gyrase_last-coot-11.pdb #6/D ASP 511 OD2 and 7z9c #2/B
MG 901 MG: 3.306Å
> select add #6/D:513@OD2
3 atoms, 3 residues, 2 models selected
> select subtract #6/D:511@OD2
2 atoms, 2 residues, 2 models selected
> distance #2/B:901@MG #6/D:513@OD2
Distance between 7z9c #2/B MG 901 MG and 2024_Gyrase_last-coot-11.pdb #6/D ASP
513 OD2: 1.968Å
> select clear
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select add #2/B:901@MG
1 atom, 1 residue, 1 model selected
> hbonds sel reveal true
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 5cdq #5/W DT 2020 O4'; 5cdq #5/U ARG 458 NE; 5cdq #5/R ARG 252
NE
0 hydrogen bonds found
> mmaker #2 to #6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2024_Gyrase_last-coot-11.pdb, chain A (#6) with 7z9c, chain A (#2),
sequence alignment score = 1974.3
RMSD between 442 pruned atom pairs is 0.931 angstroms; (across all 511 pairs:
1.676)
> show #!5 models
> hide #!6 models
> hide #6.1 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #3 models
> hide #!2 models
> mmaker #5 to #6
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2024_Gyrase_last-coot-11.pdb, chain B (#6) with 5cdq, chain C (#5),
sequence alignment score = 1647.4
RMSD between 404 pruned atom pairs is 0.883 angstroms; (across all 478 pairs:
1.624)
> show #5.3 models
> show #5.2 models
> select #5/B:508,510
16 atoms, 14 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 16 atom styles
> color sel byhetero
> select ::name="MG"
16 atoms, 16 residues, 2 models selected
> show sel & #!5 atoms
> select ::name="HOH"
308 atoms, 308 residues, 2 models selected
> show sel & #!5 atoms
> style sel sphere
Changed 308 atom styles
> select clear
> show #!2 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> hide #5.2 models
> hide #5.3 models
> show #!5 models
> show #5.2 models
> show #5.3 models
> hide #!2 models
> select #5/F
465 atoms, 501 bonds, 5 pseudobonds, 40 residues, 3 models selected
> select #5/F/E
907 atoms, 972 bonds, 6 pseudobonds, 82 residues, 3 models selected
> nucleotides sel stubs
> show sel atoms
> select clear
> select add #5/A:641@O
1 atom, 1 residue, 1 model selected
> select add #5/B:1114@O
2 atoms, 2 residues, 1 model selected
> select add #5/B:1119@O
3 atoms, 3 residues, 1 model selected
> select add #5/B:1109@O
4 atoms, 4 residues, 1 model selected
> select add #5/F:2217@O
5 atoms, 5 residues, 1 model selected
> select add #5/B:1104@O
6 atoms, 6 residues, 1 model selected
> select add #5/E:2216@O
7 atoms, 7 residues, 1 model selected
> select add #5/F:2216@O
8 atoms, 8 residues, 1 model selected
> select add #5/A:617@O
9 atoms, 9 residues, 1 model selected
> select add #5/F:2205@O
10 atoms, 10 residues, 1 model selected
> hide sel atoms
> select add #5/B:1106@O
11 atoms, 11 residues, 1 model selected
> select add #5/A:615@O
12 atoms, 12 residues, 1 model selected
> select add #5/F:2215@O
13 atoms, 13 residues, 1 model selected
> select add #5/E:2209@O
14 atoms, 14 residues, 1 model selected
> select add #5/F:2204@O
15 atoms, 15 residues, 1 model selected
> hide sel atoms
> select add #5/E:2210@O
16 atoms, 16 residues, 1 model selected
> hide sel atoms
> select up
408 atoms, 438 bonds, 36 residues, 1 model selected
> select clear
> select #5/E:MFX
29 atoms, 33 bonds, 1 residue, 1 model selected
> color sel olive
> color sel byhetero
> select clear
> color #5.2 #424242ff models
> color #5.2 #5e5e5eff models
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select add #6/D:438
4 atoms, 3 bonds, 1 residue, 1 model selected
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select #6/D:437
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/D:438
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #6/D:437
13 atoms, 11 bonds, 2 residues, 1 model selected
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select add #6/D:436
20 atoms, 17 bonds, 3 residues, 1 model selected
> select add #6/D:435
28 atoms, 24 bonds, 4 residues, 1 model selected
> hide sel cartoons
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select add #6/D:440
34 atoms, 29 bonds, 5 residues, 1 model selected
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select add #6/D:441
39 atoms, 33 bonds, 6 residues, 1 model selected
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select add #6/D:442
43 atoms, 36 bonds, 7 residues, 1 model selected
> select add #6/D:443
47 atoms, 39 bonds, 8 residues, 1 model selected
> hide sel cartoons
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/struct_measure/mouse_dist.py", line 44, in mouse_up
pick = self.session.main_view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/struct_measure/mouse_dist.py", line 44, in mouse_up
pick = self.session.main_view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> hide sel cartoons
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 151, in _redraw_timer_callback
self.session.ui.mouse_modes.mouse_pause_tracking()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 504, in
mouse_pause_tracking
self._mouse_pause()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 645, in _mouse_pause
m.pause(self._mouse_pause_position)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 803, in pause
p = self.view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>
gw.mouseReleaseEvent = lambda e, s=self: s._dispatch_mouse_event(e,
"mouse_up")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 556, in
_dispatch_mouse_event
f(MouseEvent(event, modifiers=modifiers))
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 70, in mouse_up
mouse_select(event, mode, self.session, self.view)
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/std_modes.py", line 209, in mouse_select
pick = view.picked_object(x, y)
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 838, in picked_object
p = self.picked_object_on_segment(xyz1, xyz2, exclude = exclude, beyond =
beyond,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 870, in picked_object_on_segment
p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 143, in first_intercept
pick = super().first_intercept(mxyz1, mxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 703, in first_intercept
ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2, exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 736, in _position_intercepts
p = d.first_intercept(xyz1, xyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 715, in first_intercept
p = super().first_intercept(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1069, in first_intercept
p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1086, in first_intercept_children
p = d.first_intercept(cxyz1, cxyz2, exclude=exclude)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1064, in first_intercept
p = self._first_intercept_excluding_children(mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 1108, in
_first_intercept_excluding_children
cxyz1, cxyz2 = self.positions[i].inverse() * (mxyz1, mxyz2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/place.py", line 201, in inverse
self._inverse = Place(m34.invert_matrix(self._matrix))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 141, in invert_matrix
rinv[:, :] = matrix_inverse(r)
^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 561, in inv
ainv = _umath_linalg.inv(a, signature=signature, extobj=extobj)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
numpy.linalg.LinAlgError: Singular matrix
numpy.linalg.LinAlgError: Singular matrix
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/numpy/linalg/linalg.py", line 112, in _raise_linalgerror_singular
raise LinAlgError("Singular matrix")
See log for complete Python traceback.
> select add #5/B:457
55 atoms, 46 bonds, 9 residues, 2 models selected
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mouse_modes/mousemodes.py", line 656, in <lambda>